title: Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti.
abstract: Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics.
  
  
  OBJECTIVE
  Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak of Vibrio cholerae O1 over an established time frame. By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain.
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Lee S
authors.initials: LS
authors.lastname: Katz
authors.forename: Aaron
authors.initials: A
authors.lastname: Petkau
authors.forename: John
authors.initials: J
authors.lastname: Beaulaurier
authors.forename: Shaun
authors.initials: S
authors.lastname: Tyler
authors.forename: Elena S
authors.initials: ES
authors.lastname: Antonova
authors.forename: Maryann A
authors.initials: MA
authors.lastname: Turnsek
authors.forename: Yan
authors.initials: Y
authors.lastname: Guo
authors.forename: Susana
authors.initials: S
authors.lastname: Wang
authors.forename: Ellen E
authors.initials: EE
authors.lastname: Paxinos
authors.forename: Fabini
authors.initials: F
authors.lastname: Orata
authors.forename: Lori M
authors.initials: LM
authors.lastname: Gladney
authors.forename: Steven
authors.initials: S
authors.lastname: Stroika
authors.forename: Jason P
authors.initials: JP
authors.lastname: Folster
authors.forename: Lori
authors.initials: L
authors.lastname: Rowe
authors.forename: Molly M
authors.initials: MM
authors.lastname: Freeman
authors.forename: Natalie
authors.initials: N
authors.lastname: Knox
authors.forename: Mike
authors.initials: M
authors.lastname: Frace
authors.forename: Jacques
authors.initials: J
authors.lastname: Boncy
authors.forename: Morag
authors.initials: M
authors.lastname: Graham
authors.forename: Brian K
authors.initials: BK
authors.lastname: Hammer
authors.forename: Yan
authors.initials: Y
authors.lastname: Boucher
authors.forename: Ali
authors.initials: A
authors.lastname: Bashir
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.forename: Gary
authors.initials: G
authors.lastname: Van Domselaar
authors.forename: Cheryl L
authors.initials: CL
authors.lastname: Tarr
mesh_terms: D002771:Cholera / Q000453:epidemiology* / Q000382:microbiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D058872:Epidemics; D019143:Evolution, Molecular; D023061:Gene Order; D016680:Genome, Bacterial; D006205:Haiti / Q000453:epidemiology; D006801:Humans; D009154:Mutation; D017422:Sequence Analysis, DNA; D041241:Vibrio cholerae O1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*
chemical_list: D004269:DNA, Bacterial